By type
/Controllers
/Events
/Models
By topic
/Comments
/Posts
/Users
By topic, then type
/Comments
/Controllers
/Events
/Models
/Posts
/Controllers
/Events
/Models
/Users
/Controllers
/Events
/Models
Mixed
/Comments
/Controllers
/Events
/Models
/Posts
/Users
Expanding on the "By topic, then type" idea, here is what we've done on a larger recent project, and it worked out pretty well.
/Comments
/Controllers
/CommentsController.php
/Events
/NewCommentEvent.php
Comment.php
/Posts
/Controllers
/PostsController.php
/Events
/NewPostEvent.php
/Post.php
/Users
/Controllers
/UsersController.php
/Events
/UserLoggedInEvent.php
/UserSubscribedEvent.php
/User.php